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Time-resolved SFX structure of cytochrome P450nor: 20 ms after photo-irradiation of caged NO in the presence of NADH (NO-bound state), light data
Analyse Time-resolved SFX structure of cytochrome P450nor: 20 ms after… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Y5I
- Type
- protein
- Length
- 798 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.1
- Source
- Fusarium oxysporum
- Molecule
- NADP nitrous oxide-forming nitric oxide reductase
- EC
- 1.7.1.14
- UniProt
- P23295
- Ligands
- HEM, NO
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · resolution 2.1 · 1 distinct chain · 52% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | NADP nitrous oxide-forming nitric oxide reductase (EC 1.7.1.14) | protein | 399 | 52% helix, 10% strand | P23295 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- NO · Nitric oxide · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 968 | 0.83 | 0.84 | 90 | HEM, NO, GOL |
| 2 | 1040 | 0.80 | 0.82 | 85 | HEM, NO, GOL |
| 3 | 256 | 0.54 | 0.77 | 35 | empty |
| 4 | 66 | 0.33 | 0.76 | 12 | empty |
| 5 | 55 | 0.32 | 0.77 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 461 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5Y5I · Time-resolved sfx structure of cytochrome P450NOR: 20 ms after photo- irradiation of… · the same entry in another collection · chain A against A, TM-score 1.00
- P23295 · AlphaFold monomer V2.0 prediction for NADP nitrous oxide-forming nitric oxide reductase… · a predicted model of the same protein · chain A against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P23295
- Elsewhere: RCSB PDB 5Y5I · PDBe 5Y5I · UniProt P23295
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